In Pikmin 3, all discovered Onions merge together the night after they are discovered, and become a single, universal Onion, greatly simplifying the management of Pikmin types at the beginning of each day. It also appears that the Onions in this game are much more malleable than their Pikmin and Pikmin 2 counterparts in regards to which Pikmin species they will hold. In Pikmin 3, if a new Onion color is discovered, and Pikmin from that new type are left on the landing site at the end of the day, the Master Onion there will accommodate them until the Onions fuse at the end of the day.

During the daytime, Pikmin hunt and bring food, such as pellets or slain beasts, to the Onion, which in turn produces new Pikmin seeds. If there are fewer than 100 Pikmin on the field, the seeds are ejected and take root in the ground; if not, they are stored inside the Onion, along with any other Pikmin not on the field. Unlike in the area however, the number of Pikmin that can be stored inside an Onion is unlimited.[1] When night falls and all the Pikmin have returned, the Onion folds or sucks in its legs and lifts off from the ground, joining the ship in low orbit.

Each Onion has the main body, shaped like a real world onion, with holes from which three legs come out of. At the top, there is a piece that looks like a Chaenostoma cordatum, used like helicopter blades. In the first two games, these Onions look quite organic and plain, but in Pikmin 3, they take on a more sci-fi look.

In the first two games, when night falls and all the Pikmin have returned, the Onion folds its legs and lifts off from the ground, presumably using its flower petals like rotor blades to propel itself into the low atmosphere, where it hovers until daybreak. In Pikmin 3, when it's ready to lift off, it retracts its legs back into its base and lifts off through a jet coming from the same chute it absorbs pellets and enemies the Pikmin gather.

When the Onions are first discovered in Pikmin and Pikmin 3, they are dormant. It is not known exactly what triggers this hibernation, though it's possible that a loss of Pikmin or food shortage may prompt the Onion to become dormant until conditions improve. Onions can hibernate even with the presence of their Pikmin still somewhere on the field. It seems that this dormancy does not hinder their awareness however, as the red and pink Onions are seen struggling to dislodge themselves from the traps they are found in. The Winged and Blue Pikmin species seem to have become entirely extinct by the point Pikmin 3 begins, as they are the only two species whose Onions have to sprout more of when they are reactivated.

Onions seem to have some level of sentience, in that if all Pikmin of the same color are lost, the corresponding Onion will produce a single seed the following day to prevent extinction. An Onion can also spit out a Pikmin seed if it detects that the only Pikmin available cannot be reached, as is the case when Louie first finds the red Onion in Pikmin 2. Captain Olimar notes this on his Olimar's voyage log[2]. In addition, they seem to "awaken" when a leader approaches them for the first time, and are capable of following the ship at daybreak. They know not to suck in leaders that are being carried (and to issue fireworks if that is attempted); except in one circumstance, in the bad ending of Pikmin. In Pikmin 3, the red and pink Onions struggle to break free from their respective traps.

Onions appear to require light to function, seeing as in Pikmin 3, the yellow Onion does not activate until a nearby light source is turned on, even when approached. They also seem to be able to stay underwater, at least blue Onions, as they are found underwater in Pikmin and Pikmin 3.

These bulbous plant-hives have brightly colored bodies with a black and white band across the midsection. On the top, there is a big flower, resembling the flowers that Pikmin have. There are concentric circles on the ground in the Onion landing spots in each area, which are never referred to in-game. Three stilt-like legs suspend the Onions out of the reach of hungry predators, and provide access to the inside for Pikmin. In Pikmin, Olimar states that he inspected the Onion's legs, and saw they were covered with tiny little hairs[3]. The Onions are named as such because of their resemblance to a vegetable native to Olimar's home planet[4].

In Pikmin, Onions have different appearances before they are discovered. They are darker in coloration, have no flowers on top, and are partly buried. When Captain Olimar approaches them, they explode with color, and the flower blooms and spins rapidly, pulling out the legs.

In Pikmin 3, Onions appear as small, berry-like objects with three black-metallic "joints". Out of these joints come three glowing root-like legs which allow the Onion to stand. At night, the legs completely retract and blue flames burst out of the "joints", allowing the Onion to lift off into the night sky.

When multiple Onions are discovered, they fuse together to become an even larger universal Onion that swirls different colors, depending on the type of Pikmin it holds. When all five Pikmin types in the game are discovered, the Onion swells up into a more traditional Onion-like shape.

Some of the new Onions also clearly display their Pikmin type's characteristic element upon activation: the yellow Onion creates a small burst of electricity, the blue Onion drains out a large amount of water, and the pink Onion's flower flutters erratically. The red Onion shoots out some brown particles, which might be flames, but might also be dirt lifting from the ground. The gray Onion lacks any notable reveal gimmick.

The player can access an Onion's Pikmin by having the current leader stand under the corresponding Onion's beam of light, and pressing the throw button, ( / in the first two games; / / in the third (and for the GamePad's Stylus mode)). Doing so pauses the gameplay and opens a menu where the player can choose how many Pikmin to retrieve, or how many Pikmin from the current party to place inside.

When Pikmin are told to go inside the Onion, they are dismissed from the group (bomb-rock carrying Pikmin also drop them in Pikmin and Pikmin 3), and begin climbing through the Onion's legs, eventually entering the holes the legs originate from. During this time, they can be whistled back to the group, should the player change their mind, but if not, they will be stored inside the Onion, and the field Pikmin counter will decrease. Requested Pikmin will come out of the Onion from the same holes, and slide down the legs. If the leader is close enough, they will also automatically come to their side. In the case that there are Pikmin of multiple maturities, flower Pikmin will be withdrawn first, until there are no more left, in which case bud Pikmin will be withdrawn, and finally leaf Pikmin. This is not true when Pikmin go inside the Onion – all Pikmin sent inside will go in in a random order.

The yellow Onion stores Yellow Pikmin, and is the second type the player will come across in the first game. In Pikmin, it is found dormant in The Forest of Hope amidst several yellow Pellet Posies and free-standing yellow pellets. In Pikmin 2, the yellow Onion is located in the Perplexing Pool behind a poison gate protected by a Fiery Bulblax, so White and Red Pikmin are required to reach it. There are a few yellow Pellet Posies nearby which will not regrow once they've been harvested. In Pikmin 3 the Yellow Onion is discovered by Brittany in a cave, as soon as the Distant Tundra is entered. To activate it, the Yellow Pikmin nearby must be thrown at a generator, in order to create a current that lights a light bulb, awakening the Onion.

The blue Onion houses Blue Pikmin, and is the last type to be discovered in all three games. In Pikmin, the blue Onion can be found in The Forest Navel in a pool near the landing site. Several blue Pellet Posies are in the immediate vicinity, as well as a free-standing blue 5 pellet. In Pikmin 2, the Blue Onion is located in the Awakening Wood; although it can be seen relatively early in the game, it lies behind an electric gate, meaning that Yellow Pikmin from the Perplexing Pool are required to access it. A small pool blocks the only direct path up to the gate, so the Pikmin must be thrown onto a nearby ledge (while taking care not to disturb the Cloaking Burrow-nit lying in wait there). The leader can then walk around through some water to reach them, and order them to defeat the beast and demolish the gate, allowing him to find the game's first five Blue Pikmin. In Pikmin 3, the blue Onion is located in a pool at the Garden of Hope and can only be accessed after defeating the Scornet Maestro at Twilight River.

For some unknown reason, when landing on an area in Pikmin and Pikmin 2, the Blue Onion seems to hover a bit before landing, therefore landing after the red and yellow Onions.

The gray Onion is the Onion that holds Rock Pikmin. It can be found in the Garden of Hope, right in the cave next to the area in which Brittany was being held. A Medusal Slurker guards the crystal holding the gray Onion, and it is holding six Rock Pikmin inside of it. Near the gray Onion there are 3 crystals, two of which hold 1-pellets, and the last of which holds a Data File explaining how carrying works with multiple types of Pikmin holding the object. The Medusal Slurker can also be carried back to the Onion.

The pink Onion is home to the Winged Pikmin. Upon reaching the Twilight River and walking around, the player will get a cutscene showing that the pink Onion is trapped in an Arachnode web. However, the Onion is located across the River, and a rather large bridge must be build across it to reach the other shore. Once the Onion is freed from the web, it will spit out one Winged Pikmin seed. Near the Onion are many Flukeweeds, which hold 1-pellets, 5-pellets, nectar eggs, and Female Sheargrubs underneath them. There is also a glitch that allows the player to reach the other shore without the need to build the bridge, though it is recommended as it will help with carrying back objects.

In Pikmin 3, the gray Onion fuses with the red Onion at the end of the day in which the player discovers Rock Pikmin to form a larger, universal "Master Onion" that holds all Pikmin types. As the player discovers the remaining Pikmin types, their Onions fuse into the Master Onion as well. The Onion menu has been changed as a result, now allowing the player to pick the numbers for all types at once. The majority of one type of Pikmin carrying an object to the Onion will determine which type of Pikmin the Onion produces. For example, if ten Rock Pikmin and five Red Pikmin are carrying a Red Bulborb to the Onion, Rock Pikmin will be produced. This compound Onion is never given an official name, but is commonly referred to by fans as "Master Onion".

Warning: the following text contains major spoilers about the ending in Pikmin.

Four pink Onions, four black, two cyan, one orange, one blue, one green and one purple. They appear during the "good ending" in Pikmin.

In the best ending of Pikmin, there is a scene where fourteen Onions, including colors that have not appeared in a Pikmin game so far, fly above the Planet of the Pikmin. It is unknown whether they are trying to follow Captain Olimar, or merely hovering for the night. Interestingly, one of the Onions seen is purple, and Purple Pikmin were indeed introduced in Pikmin 2, but without an Onion.

In Pikmin 2's 2-Player Battle and Pikmin 3's Bingo Battle, each player has one Onion in their base. These Onions act slightly different: they can't store extra Pikmin, and leaders cannot take Pikmin out or put them in. They also spit out the same amount of Pikmin lost to enemy Pikmin, without the need of nutrients.

In Pikmin 2, the first player gets a red Onion, while the second player owns a blue Onion. In Pikmin 3's the first player gets a cyan-colored Onion that pulses yellow, and the second player gets a pink-colored Onion that pulses orange.

The number of Pikmin created when a pellet is delivered to an Onion is larger if the pellet type matches the Onion's. This should be taken into account when ordering Pikmin to carry a pellet, in order to maximize the number of Pikmin obtained.

When the Onion generates Pikmin, in order to save time, like on a speedrun, it is best to withdraw Pikmin from Onions so that the field total reaches 100. This is because the Pikmin will be expelled as seeds in case there are less than 100 Pikmin on the field. The process of waiting for the seeds to be expelled and planted, waiting for them to grow stems, and plucking them is quite lengthy. The time it takes to withdraw the Pikmin that cap the counter, and in the case of the new Pikmin being a different type, the time it takes to store them again and retrieve the new Pikmin, is considerably smaller overall. In speedruns, the route is normally planned out so that, whenever possible, the field counter is capped when new Pikmin are generated. Normally, it's also organized so that no time is wasted withdrawing Pikmin just to avoid plucking the new ones.

In Pikmin 2, after the Five-man Napsack has been obtained, the Pikmin can be told to carry a lyingleader to an Onion if the player holds / . This carries the advantage of having one leader go to an Onion automatically while the player can control the other leader, which increases the multitasking potential. This can also be done in the first game, by holding / , but because there is only one leader, the multitasking advantage does not exist. This feature has been removed in Pikmin 3 in favor of the Go Here! command on the KopPad.

In Super Smash Bros. Brawl and Super Smash Bros. for the 3DS, the three main Onions appear on the Distant Planet stage, and in the case of Brawl, as a random trophy too. On the arena, when a pellet is thrown into one, items are ejected. The higher the number on the pellet thrown, the higher the amount of items that will appear, with even more items appearing if the pellet and Onion have the same color, similar to the way it works in the Pikmin games. The Onions randomly land and fly away, but can be forced to leave early if hit several times. In Brawl, a red Onion also appears as a sticker.

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Items considered to be the places where Pikmin are born. As to the actual biology of the process, much is still unclear. Onions absorb the prey that Pikmin capture and use it to produce new Pikmin. In addition, Onions can take in Pikmin and later release them. These organisms are crowned with distinctive propeller-like sets of leaves that spin around, enabling them to fly.

When Olimar first came upon the Red Onion in Pikmin, he was knocked over by one of the legs as it sprang out of the ground. When he finds the other two later on in the game, he is a little more cautious and backs away.

In Pikmin, attempting to take out more Pikmin from a blue Onion than are in it results in the erroneous message "There are no blues Pikmin to take out." The message should be, "There are no blue Pikmin to take out."

Unused content in Pikmin 2 reveals that the Onions were originally planned to have a "booting up" cutscene, just as they did in the first game. These cutscenes can be found almost entirely finished inside the game.

If, on a day where Olimar or Louie finds an Onion, a cave is entered after whistling the wild Pikmin, the Onion will be at the landing site when the cave is left.

It is possible to whistle the Pikmin as they are exiting the Onion. While mostly aesthetic, this can be used to bring a Pikmin to the party slightly faster than normal. In Pikmin, the Pikmin will rarely react to the whistle, while in Pikmin 2, they'll react to it almost every time.

If the player looks up at the Master Onion in Pikmin 3 with the KopPad, they can see what appears to be solar panel-like cells on its petals.

Alph mentions in a log entry that the swirling colors of the Master Onion may actually be the Pikmin themselves, stored in a simpler, fluid form for easier storage.

When the master Onion in Pikmin 3 receives nutrients from a second type of Pikmin while already producing seeds from a first type, it will not produce more than one type of Pikmin at once. It will finish producing the first type of Pikmin before moving to a different type.

In Pikmin 2, one can hear idle Pikmin noises coming from the Onions and the Hocotate ship.